getSequencingBias: 'getSequencingBias'

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

getSequencingBias

Description

getSequencingBias takes the output of peak calling with callOpenTiles and creates sample-tile matrices containing the signal intensity at each tile.

Usage

getSequencingBias(
  SampleTileObj,
  cellPopulations = "all",
  cellPopulation,
  groupColumn,
  foreground,
  background,
  verbose = TRUE
)

Arguments

SampleTileObj	a SummarizedExperiment object generated by MOCHA
cellPopulations	vector of strings. Cell subsets found in the TSAM, or the word 'All' if all should be used.
cellPopulation	A string denoting the cell population of interest
groupColumn	The column containing sample group labels
foreground	The foreground group of samples for differential comparison
background	The background group of samples for differential comparison
verbose	Set TRUE to display additional messages. Default is FALSE.

Value

plot object

MOCHA documentation built on May 29, 2024, 2:25 a.m.